Find research datasets worth reusing

opencc-zeroJun 2022View details →

Joining forces in Ochnaceae phylogenomics: A tale of two targeted sequencing probe kits

Premise: Both universal and family-specific targeted sequencing probe kits are becoming widely used for the reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships. Methods: We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit, and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support. Results: For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. The merging of data obtained with the two kits resulted in a well-supported phylogenetic tree. Conclusions: The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family-specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.

opencc-zeroJun 2022View details →

Whole-transcriptome sequencing identifies neuroinflammation, metabolism and blood-brain barrier related processes in the hippocampus of aged mice during perioperative period

Aim: Perioperative neurocognitive disorders (PND) occur frequently after surgery and anesthesia, especially in aged patients. Previous studies have shown multiple PND related mechanisms in the hippocampus, however, their relationships remain unclear. Meanwhile, the perioperative neuropathological processes are sophisticated and changeable, single period study could not reveal the accurate mechanisms. Thus, multiperiod whole-transcriptome study is necessary to elucidate the gene expression patterns during perioperative period. Methods: Aged C57BL/6 mice were subjected to exploratory laparotomy under sevoflurane anesthesia. Whole-transcriptome sequencing (RNA-seq analysis) was performed on the hippocampi from control condition (Con), 30 minutes (Day0), 2 days (Day2) and 7 days (Day7) after surgery. Gene Ontology/Kyoto Encyclopedia of Genes and Genomes analyses, quantitative Real-Time PCR, immunofluorescence and fear conditioning test were also performed to elucidate the pathological processes and modulation networks during the period. Results: Through RNA-seq analysis, 328, 3597 and 4179 differentially expressed genes (DEGs) were screened out in intraoperative period (Day0 vs Con), early postoperative period (Day2 vs Day0) and late postoperative period (Day7 vs Day2). The involved GO biological processes were divided into 9 categories, and positive-regulated processes were more than negative-regulated ones. Seventy-four transcription factors were highlighted. The potential synaptic and neuroinflammatory pathways were constructed for Neurotransmitter, Synapse and Neuronal alteration categories with 9 DEGs (Htr1a, Rims1, Ezh2, etc.). The metabolic and mitochondrial pathways were constructed for Metabolism, Oxidative stress and Biological rhythm categories with 9 DEGs (Gpld1, Sirt1, Cry2, etc.). The blood-brain barrier and neurotoxicity related pathways were constructed for Blood-brain barrier, Neurotoxicity and Cognitive function categories with 10 DEGs (Mmp2, Itpr1, Nrf1, etc.). Conclusion: The results revealed gene expression patterns and modulation networks in the aged hippocampus during perioperative period, which provide insights into overall mechanisms and potential therapeutic targets for prevention and treatment of perioperative central nervous system diseases, such as PND, from the genetic level.

openJun 2023View details →

Consensus nucleotide sequences for env and gag for paper: Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models

This is the consensus sequence repository to the manuscript "Insights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models". It contains the 10% consensus nucleotide sequences of the env and gag (only p24) protein of HIV-1 used for the training and leftout data set. The NGS sequences are available under BioProject ID PRJNA810303 and the corresponding BioSample Accession IDs are SAMN26241863:26242168 and SAMN28728524:SAMN28728529 <ul> <li>env_leftout.fasta <ul> <li>A fasta file that contains the consensus nucleotide sequences for the env protein for the leftout data set</li> </ul> </li> <li>env_nt_274.fasta <ul> <li>A fasta file that contains the consensus nucleotide sequences for the env protein for the training data set</li> </ul> </li> <li>gag_leftout.fasta <ul> <li>A fasta file that contains the consensus nucleotide sequences for the gag protein for the leftout data set</li> </ul> </li> <li>gag_nt_274.fasta <ul> <li>A fasta file that contains the consensus nucleotide sequences for the gag protein for the training data set</li> </ul> </li> </ul>

Sequencing summaries from pfhrp2 detection and characterization using the MinION sequencer

This dataset comprises sequencing summaries generated by the MinKnow software during sequencing runs related to the project "Portable and cost-effective genetic detection and characterization of Plasmodium falciparum hrp2 using the MinION sequencer."  This dataset was used in the generation of figures for the manuscript related to this project, and can be used with the Jupyter Notebook for figure generation provided in the project's <a href="https://github.com/sjsabin/minion_hrp2_project">github</a>.

Distance matrix for UNITE sequences

Flattened and compressed version of 2 pairwise distance matrices corresponding to <a href="https://doi.org/10.15156/BIO/1264708">this</a> UNITE release. Can be imported in a pipeline for building an overarching fungal phylogeny for UNITE (<a href="https://github.com/luukromeijn/MDDB-phylogeny">Github source code</a>).  Importing might take up to an hour, but this is still much quicker than the 36-hours pairwise distance calculation.  The 6-mer Google distance is way more accurate than the w-metric, so we highly recommend using the 6-mer Google distance. More documentation can be found <a href="https://github.com/luukromeijn/MDDB-phylogeny#readme">here</a>.

Liu_et_al_DMG_In Situ Sequencing_expression_maps

This repository includes the In Situ Sequencing datasets (HybISS) generated for Liu et al. 2022. Both gene expression maps (reads.zip) as well as cell type maps (this is, after segmenting individual cells) are included. Malignant cell types were assigned based on probabilistic cell typing by ISS (Qian et al. 2020) and can be found at celltyping_malignant.zip. Healthy cells, in addition to the described malignant ones, were included in celltyping_malignant_and_healthy.zip. In addition annotated data objects (anndata) were generated for all 16 samples (anndata_objects)

opencc-zeroJul 2023View details →

Long-read-based draft genome sequence of Indian black gram IPU-94-1 'Uttara': Insights into disease resistance and seed storage protein genes

Black gram [Vigna mungo (L.) Hepper var. mung<a>o</a>] [LAV1] is a warm-season legume highly prized for its protein content along with significant folate and iron proportions. To expedite the genetic enhancement of black gram, a high-quality draft genome from the center of origin of the crop is indispensable. Here, we established a draft genome sequence of an Indian black gram cultivar, 'Uttara' (IPU 94-1), known for its high resistance to mungbean yellow mosaic virus. Pacific Biosciences of California, Inc. (PacBio) single-molecule real-time (SMRT) and Illumina sequencing assembled a draft reference-guided assembly with a cumulative size of ~454.4 Mb, of which, 444.4 Mb was anchored on 11 pseudomolecules corresponding to 11 chromosomes. Uttara assembly denotes features of a high-quality draft genome illustrated through high N50 value (42.88 Mb), gene completeness (benchmarking universal single-copy ortholog [BUSCO] score 94.17%), and low levels of ambiguous nucleotides (N) percent (0.0005%). Gene discovery using transcript evidence predicted 28,881 protein-coding genes, from which, ~95% were functionally annotated. A global survey of genes associated with disease resistance revealed 119 nucleotide binding site–leucine rich repeat (NBS-LRR) proteins, while 23 genes encoding seed storage proteins (SSPs) were discovered in black gram. A large set of microsatellite loci were discovered for marker development in the crop. Our draft genome of an Indian black gram provides the foundational genomic resources for the improvement of important agronomic traits and ultimately will help in accelerating black gram breeding programs.

opencc-zeroJul 2022View details →

Amino acid sequences of RWP-RK domain containing proteins used for the construction of phylogenetic tree shown in Fig. 1

The RWP-RK protein family is a group of transcription factors containing the RWP-RK DNA-binding domain. The RWP-RK DNA-binding domain is an ancient motif that emerged before the establishment of the Viridiplantae (green plants), which consist of green algae and land plants. This domain is mostly absent in other kingdoms but widely distributed in Viridiplantae. In green algae, a liverwort, and several angiosperms, RWP-RK proteins play essential roles in nitrogen responses and sexual reproduction-associated processes, which are seemingly unrelated phenomena but possible interdependent processes in autotrophs. Consistent with related but diversified roles of the RWP-RK proteins in these organisms, the RWP-RK protein family appears to have expanded intensively, but independently, in the algal and land plant lineages. Therefore, bryophyte RWP-RK proteins occupy a unique position in the evolutionary process of establishing the RWP-RK protein family. In this review, we summarize current knowledge about the RWP-RK protein family in the Viridiplantae, and discuss the significance of bryophyte RWP-RK proteins in clarifying the relationship between diversification in the RWP-RK protein family and procurement of sophisticated mechanisms for adaptation to the terrestrial environment.

opencc-by-4.0Apr 2022View details →

Discovering molecular regulators of ageing using mixture models with RNA-sequencing data

Identifying the molecular regulators that control ageing is challenging because the ageing process is influenced by a combination of genetic and environmental factors which makes it difficult to source the contribution of a single gene. Multiple studies have demonstrated that as humans age, increased gene expression heterogeneity results in the dysregulation of key regulators and pathways. Given the dynamic nature of gene expression, it is vital that this data be modelled by statistical approaches that can appropriately account for changes in variability to understand the contribution of heterogeneity during the aging process and properly identify its regulators. This study demonstrates the utility of using mixture models to model biological variability of gene expression occurring during ageing and how novel potential regulators of ageing can be identified. Our mixture modelling approach was applied to gene expression data from the Genotype-Tissue Expression (GTEx) cohort. For every gene, the expression profile was modelled using a mixture model across the cohort where the subset of donors corresponding to each mode was tested for a significant change in age group. The multi-tissue aspect of GTEx was leveraged to find ageing regulators based on this mixture model approach genes that were common across multiple tissues, suggesting that the regulation of ageing may also be controlled through a set of genes that have non-tissue-specific activity. Our approach identified well-documented ageing regulators mTOR and RICTOR and other potential ageing regulators such as IL4 and GPR4 which were detected only by our approach. Genes identified by edgeR, DESeq2 and the mixture model-based approach were enriched for similar biological pathways. This suggests that while the specific ageing regulators identified from our approach may be distinct, they generally belong in the same pathways as the genes identified by standard approaches. Overall, these results indicate that modelling gene expression variability using mixture models in conjunction with standard differential gene expression can help uncover new regulators that have a potential role for understanding human ageing. I

Whole genome sequence variant discovery from Ethiopian Boran, N'Dama and Holstein cattle

Whole genome sequence variants (SNPs) from forty samples of each Ethiopian Boran, N'Dama and Holstein cattle breeds which were utilised in the Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle study by Riggio et al., 2022, (in review). The NDama sequences included samples from Guinea (n =21), Nigeria (n =10) and Senegal (n = 9); and the Boran samples from Ethiopia (n = 30) and Kenya (n = 10). Variants discovery followed the protocol described in the Material and Method section of the paper.

opencc-zeroJul 2022View details →

ARPIP: Ancestral sequence Reconstruction with insertions and deletions under the Poisson Indel Process

Modern phylogenetic methods allow inference of ancestral molecular sequences given an alignment and phylogeny relating present day sequences. This provides insight into the evolutionary history of molecules, helping to understand gene function and to study biological processes such as adaptation and convergent evolution across a variety of applications. Here we propose a dynamic programming algorithm for fast joint likelihood-based reconstruction of ancestral sequences under the Poisson Indel Process (PIP). Unlike previous approaches, our method, named ARPIP, enables the reconstruction with insertions and deletions based on an explicit indel model. Consequently, inferred indel events have an explicit biological interpretation. Likelihood computation is achieved in linear time with respect to the number of sequences. Our method consists of two steps, namely finding the most probable indel points and reconstructing ancestral sequences. First, we find the most likely indel points and prune the phylogeny to reflect the insertion and deletion events per site. Second, we infer the ancestral states on the pruned subtree in a manner similar to FastML. We applied ARPIP on simulated datasets and on real data from the Betacoronavirus genus. ARPIP reconstructs both the indel events and substitutions with a high degree of accuracy. Our method fares well when compared to established state-of-the-art methods such as FastML and PAML. Moreover, the method can be extended to explore both optimal and suboptimal reconstructions, include rate heterogeneity through time and more. We believe it will expand the range of novel applications of ancestral sequence reconstruction.

A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems

Sequence alignment is a fundamentally memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory architectures alleviate this bottleneck by providing the memory with computing competencies. We propose Alignment-in-Memory (AIM), a framework for high-throughput sequence alignment using processing-in-memory, and evaluate it on UPMEM, the first publicly-available general-purpose programmable processing-in-memory system.

opencc-by-4.0Dec 2021View details →

Plasmid Sequences for Brophy et al., 2022: Synthetic genetic circuits as a means of reprogramming plant roots

Plasmid Sequences for Brophy et. al. 2022: Synthetic genetic circuits as a means of reprogramming plant roots

Script and single cell RNA sequencing datasets of Biomphalaria glabrata hemocyte

The results of the gene and cell barcode counts (feature-barcode matrices) are available in the file "filtered_feature_bc_matrix_Naive". These data have been processed by cellRanger v3.1.0 and can be used with the script "scRNAseq_Biomphalaria_naive" which gathers all the analyses done for publication.

Draft Genome sequencing of Nocardia sp. strain WB46 Isolated from Salix purpurea Growing in a Site Chronically Contaminated by Petroleum Hydrocarbons

Assembled contigs of the genome of Nocardia sp. strain WB46 isolated from the rhizosphere of Salix purpurea growing in a site chronically contaminated by petroleum hydrocarbons located at Varennes, Qubec, Canada.

opencc-by-4.0Apr 2022View details →

Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation

SNV of 23 parental barley inbreds of the double round robin population (DRR) (<a href="https://doi.org/10.1111/pbi.13746">https://doi.org/10.1111/pbi.13746</a>) used in the publication "Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation". SV, INDELs, and additional data are available via figshare (https://doi.org/10.6084/m9.figshare.16802473).

Supplementary Data for "The shaky foundations of simulating single-cell RNA sequencing data"

Supplementary Data for "The shaky foundations of simulating single-cell RNA sequencing data" See description.txt, Supplementary Text, Methods and https://github.com/HelenaLC/simulation-comparison for further description of the files available here.

Sequence tracks of Ago2 Neural stem cells and differentiated neurons from single-cells- Related to Fig. 5

Single neural stem cells were isolated from the Hippocampus of newborn mice generated from a hybrid cross. Some of these cells were differentiated In vitro and either the NSC or differentiated neurons were lysed and underwent a reverse transcription. The newly formed cDNA was used as a template to amplify expressed Ago2 transcript which was then sent off for Sanger sequencing. A SNP located within the exon was used to determine whether the transcript from that cell was generated from the maternal or paternal allele.

Sensitivity-enhanced multidimensional solid-state NMR spectroscopy by optimal-control-based transverse mixing sequences

The dataset here contains the raw data and pulse programs used for the publication "Sensitivity-enhanced multidimensional solid-state NMR spectroscopy by optimal-control-based transverse mixing sequences" submitted to JACS. All data is in a native Bruker TopSpin format. Data is organized in folders corresponding to Figures of the original publication. Detailed description is included in the file description.txt. We reccomend to visit our website optimal-nmr.net for additional information about optimal control methods applied to pulse sequence development for solid-state magic-angle-spinning NMR studies of proteins.